Naruto The Mad Scientist
by ShadowKnight07
Summary: Naruto the second coming of Orochimaru. - Strong/Dark Naruto. - Doujutsu? - Naruto X ? Pairings are undecided. !Hiatus!
1. Chapter 1

HeLLo everyone,

I will try making this fanfic realistic as possible and I am asking one thing in return and that is **Review!**

Quote of the chapter:

"What we call the beginning is often the end. And to make an end is to make a beginning. The end is where we start from."

T.S. Eliot

**DISCLAIMER!**

I don't own Naruto, if I did why in the hell I would be writing on here.

**.:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:.**

**Chapter One: End and New Beginning.**

He is been hated, beaten, burned, stabbed, poison, and almost killed many times. Naruto knew everyone hated him but he didn't know why they hated him but every time when people glared at him or beaten him, he started to hate them is well. He started to grow darker but he never let anyone know about it, he just used his mask to cover his darkness.

He wore a black t-shirt with leaf sign in the middle that it was red colour and black shorts that it was dirty.

As he was walking around the village, he could feel the glare that the villagers giving him, making him feel hatred and anger and he though what did he do to deserve this. He ran to the only place he felt safe, to the forest. When he arrived at the forest, he could feel safe here because no one came here; this forest was right next to forest of death.

Naruto started walk around the forest, he was asking himself, why, what did he do to deserve all this treatment, he might have been six years old but from what people did to him, grow more mature than anyone else then in his age.

He was cursing the villager and kicked the dust of floor from the anger but something else flew away, it was like paper with signs and some writing on it, then hatch appeared where he kick the sign off, but it was hard to see the hatch. Naruto took the sign paper then open the hatch and enter the place. It was like a base, from the stories that he read. Naruto started to walk around and see what this place was, after he looked around the base, he notice this place was some kind of a lab like in the hospital, there was many scrolls about experiments, ninjutsu, kin-jutsu and other stuff that he didn't bother to read yet. There were many body parts inside the glass jars with some kind liquid inside it.

Naruto start to checking the scrolls and end of the every scroll, there was the same name, writer's name, Orochimaru. Naruto though himself that this men must be some kind of genius and he should do some research about him. One of the scrolls he checked there was information about the sign paper that he kicked, it turns out that the sign paper was a seal to keep this place hidden and invisible. Naruto though that he shouldn't lose this seal paper because he will need to make this place hidden when he isn't around.

Naruto took some scrolls with him and exist the base. Then he closed the hatch and sticks the paper on it then it went invisible. Naruto look around for a minute then made his way back to his home or the way he called it, 'the shit hole'.

**.:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:.**

Time Skip: 1 year later.

Naruto was now seven years old, he start to learn about chakra control and medical jutsus because of the beaten he gets from the village population and he carry around a waist bag with him that had some medical equipment. One more year and he can finally start the academy and become ninja.

While Naruto was wondering around the river, he notice that there was a man floating. After few minutes he finally pulled the man off the river, he notice that the man's right eye was removed and he was dying. Naruto caught the glimpse of the man's red eyes. He pushed the eyelids to see the eye clearly. In few seconds he noticed what it was. He seen this eye in many scrolls he found it in the lab, it was one of the Three Great Dōjutsu. It was Sharingan.

He was surprised to found one that already had three tomoe's. He smiled that finally kami start to give him some luck. He knew someone already taken the right eye so if he took it then throw the man back in the river; people think that the man who killed him took both of his eyes. Naruto just did what he just thought. He took out his medical equipment and removed the eye then sealed it away in a storage seal that he found it in the lab. Then he throw the man back in to river, and start to rush back to lab to put eye in jar with liquid that keep the cells in the eye alive

Naruto came to his lab and put the eye in jar with the liquid. He knew all about the sharingan from his studies in the lab but he couldn't just switch his eye with the sharingan. Of course he knew that there will be no way that he can explain how he had the sharingan and even he had his eye covered, there will be question from Hokage, that what happen to his eye so he just left the eye in jar until it's time.

**.:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:.**

Hmmmm. Finally first chapter's finish and there will be more coming. I already started on the new chapter. If you have any complaints about my spelling or grammar stuff then leave a review but you don't like my story then leave, don't leave a review because I am doing this for my own pleasure and I ain't getting paid for it so that I can't take your shit.

Naruto X ? = well I am not sure about the pairings so I will be waiting for your reviews on this matter.


	2. Chapter 2

**HeLLo everyone,**

I will try making this fanfic realistic as possible and I am asking one thing in return and that is **Review!**

**Quote of the chapter: The Mask**

every day  
when I get dressed  
I put on something  
besides the usual rest

its not made of wool  
yet underneath it I sweat  
no one can see it  
even if id let

its very delicate  
yet it doesn't brake  
its quite small  
yet it no one can take

it smells like guilt  
it feels like mystery  
it tastes like sweat  
it hides me history

**DISCLAIMER!**

I do not own Naruto, if I did why in the hell I would be writing on here.

**.:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:.**

**Chapter One: ****Genin Teams.**

**Time Skip: 5 years Later**

It was already been six years since he found the Orochimaru's lab. Since then a lot of things changed about Naruto, he started to train with scrolls that he found in the lab and master some ninjutsu, kin-jutsu, and fūinjutsu. Unlike what scroll said about fūinjutsu being hard to master but Naruto done it with not too much effort, as if this was in his blood.

Academy was not much of a problem, of course teacher didn't teach him anything important or teach him to do it the right way but he already know most of the stuff from the scrolls he had in the lab or when he secretly broke in the library and stole some of the history books and some academy level ninjutsu scrolls.

Yesterday, Nauto passed the Genin exam. Today was Genin team placement day so everyone was excited. Naruto sat at the back of the class room. He wore a plain black hoodie, plain black cargo pants, black shinobi sandals, and black fingerless gloves. To keep up the good relationship with the Hokage, Naruto all ways visited the old man, acting happy around him and making sure that he isn't suspicion of anything.

In his time in academy, Naruto tried to not to stand out a lot and passed exam with normal scores, they weren't low but they weren't high either.

When Naruto was lost in his thoughts, Iruka and his assistant Mizuki enter the class room. There was just too much noise, girls were fighting over, who was going to seat next to Sasuke. Naruto never understood why did the girls like this guy some much, he wasn't that special.

Iruka tried to stop the shouting by trying to talk to them but he couldn't even hear what he was saying. Then Iruka got mad and used his special jutsu, **Big Head no jutsu. **"Shut up!" Iruka yelled.

Class room went silent. "Okay everyone, first I would like congratulate all of you for passing your exam and becoming genin." Iruka expressed it with smile.

"Now, today you all know that we are here to tell you, your team placements. Team 1..." Iruka started to name the team member and there team number.

"Okay, Team 7 Sasuke Uchiha" When Sasuke name read, all girls went quit and start to praying god to be on his team.

"Sakura Haruno" The moment he said her name, she just jump up and doing some kind of a victory dance. Some of the girls started whisper curses but they didn't lose hope there was still one more place.

"Naruto Uzumaki." Iruka said and some of the fan girls started to cry.

"and your sensei would be Kakashi Hatake" Iruka finished team 7

'So my new team-mates are arrogant bastard and weak shit female.' Naruto thought to himself with pissed of face.

Sakura was still celebrating her, so called victory and didn't even hear the third members name. Sasuke just said "Hn".

Everyone went silent and Iruka continued, "Team 8, Hinata Hyūga, Shino Aburame, and Kiba Inuzuka. Your sensei would be Kurenai Yūhi". Kiba smiled hearing the name of the Hinata but she look disappointed.

"Team 9, its still undecided".

"Team 10, Chōji Akimichi, Shikamaru Nara, and Ino Yamanaka. Your sensei will be Asuma Sarutobi." He finished reading teams. Choji and Shikamaru noded each other with smile. Ino was asking kami, what did she do to deserve this.

"Okay, just wait for you sensei's here, they will come to pick you guys up." Iruka said and left the class.

Few minutes later Asuma Sarutobi came and picked his team. Other sensei's came and pick there team is well then Kurenai Yūhi came pick her team up and left.

**Time Skip: Three Hours Later**

It was already been three hours, Naruto was getting impatient but he didn't show it outside, unlike others. Sakura was trying to talk to Sasuke, but the only answer she was getting, was 'hn' or just ignoring her.

'Shit, when is this ass-hole is going to come." Naruto though.

When Naruto got up to leave, man enter the room, he had gray hair, one eye cover and he had dark blue shinobi clothes.

"Meet me at top of the academy building." He said just before turning into white smoke cloud.

**.:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:.**

"Okay, Lets start by introducing our self." Gray hair guy said.

"We already know some about each other so why don't you start first sensei." Pink hair girl asked.

"Hmm. My name is Kakashi Hatake, my likes are... I don't feel like telling, my dislike are... none of you business, Dream for future... I don't have any, Hobbies... well I have a lot." Gray hair men finished.

'So he is lazy, well I don't really care, I can teach my self better anyway." Naruto though

"Pinkie, it's your turn." Kakashi said.

"Well, my name is Sakura Haruno, My likes are..."She stop look at Sasuke and giggled, "My dislike are people who try to act cool like Sasuke. My dream is..." She look at Sasuke again and giggled. "And my hobbies are, gardening and thinking about Sasuke." She finished with that.

'So she is a fan girl like the report said about her.' Kakashi thought with depressed expression.

"Your turn kid." He said and pointing at Sasuke

"My name is Sasuke Uchiha, I don't have many thing that I like, I pretty much dislike a lot things, my hobbies are training, My dream is... no... My ambition is to kill a certain man and revive my clan."

'An avanger...' Kakashi thought

"Your turn, kid in black" He said and turn to Naruto.

Sasuke and Sakura turn is well because they didn't know much him. Only thing they knew was, for some reason adults hated him.

"My name is Naruto Uzumaki. My likes are Training, learning new things and ramen. My dislikes are... there isn't much. My hobbies are reading. My dream is undecided.

'So this is the Jinchūriki.' Kakashi thought.

"Okay then meet me tomorrow at traning ground 7 in 6:00 am for your exam and don't eat anything."

All of the three genins looked confused, "Sensei we passed the exam." Sakura pointed out.

"Sakura that was only exam to see if you have requirements but this is a test to see if you can be genin and if you fail you will be send back to academy." After he finished he had a evil smiled that they can see it from the shape of the mask.

"So what's the chance of us passing?" Naruto asked

"Well 66% of the all graduates will fail so you guys have 33.3% chance of passing." He said then he used Body Flicker Technique and left.

All of the team members were surprised by the new exam, it was Sakura who first shook off the shock.

"Say Sasuke, do you want to go on a date with me?" Sakura asked but Sasuke ignore the question and turn to his other team mate but he was already gone.

**.:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:.**

Naruto arrived at his lab. 'I still got some time, I should carry on working on the curse seal." Naruto thought. Three years ago he found a scroll in the lab about curse seals. He read the scroll and learned that this seal can give people power. So he started to learn about it then when he learn everything, he started make his own curse seal from Orochimaru's notes. 'Just few more days and it will be finished.' Blonde thought.

**.:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:.**

**End of the Chapter...**

Finally second Chapter is finish. I will update third chapter tomorrow. I will waiting for your review so please don't forget leave a review

Naruto X ? = well I am not sure about the pairings so I will be waiting for your reviews on this matter.


	3. Chapter 3

**HeLLo everyone,**

I will try making this fanfic realistic as possible and I am asking one thing in return and that is **Review!**

**Quote of the chapter:**

"Coming together is a beginning, staying together is progress, and working together is success." Henry Ford

**DISCLAIMER!**

I do not own Naruto, if I did why in the hell I would be writing on here.

**.:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:.**

**Chapter One: ****Exam.**

Naruto worked on his curse seal all night, and finally after three years hard work Naruto finished it but he didn't apply on himself, if he did, he had to lock himself up and let curse seal become part of his soul and this progress is very painful.

Naruto left his lab and made his way to the training ground. When he arrived Sakura and Sasuke was already there. Naruto didn't say anything and just sat down by the tree. Sakura was busy to notice Naruto arrival, like always she was asking Sasuke on date but it didn't look like it's was going well.

**.:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:.**

**Time Skip: Three Hours.**

Naruto was really pissed off, he never like people who kept him waiting but he kept his cool. Sasuke was laid on the grass and his hands behind his head, watching sky but his eye kept twitching. Sakura was going berserk, about how can he kept waiting all mighty last Uchiha.

Suddenly Kakashi pop out in front of the team seven. Before anyone can say something, Sakura yelled, "How dare you Kakashi-sensei, how can you make my Sasuke-kun and me wait."

"Sorry Sakura, I had to help an old lady."

They knew he was lying from his sarcastic voice he used.

"Whatever. Can we start the test now?" Sasuke said while trying to keep his cool

"Of course" Kakashi said and pull out two bells

"Test is quite simple, three of you attack me and who ever get the bells passes"

"But sensei there is only two bells." Pink haired girl pointed out

Kakashi eye smiled, "Yes, only two of you will pass."

Naruto was confused, he never heard of three man team. 'Hmm, there must be some kind of catch here.' Naruto thought.

Sakura's smile got even bigger, 'This is even better, without that creepy Naruto, me and Sasuke-kun have some more privacy.'

'One of going to fail? I remember father telling me, teams always been four people.' Sasuke was thinking but it got broken by Kakashi's start signal.

"Well then let us start." Kakashi said and all three students disappeared into the forest.

Sakura was busy looking for Sasuke, so that they can team up and pass together and live happily even after. Sasuke was hidden quite good and looking at Kakashi and waiting for an opening. Naruto went little bit far away from Kakashi to think about what was he planing.

Kakashi took out his **HOLY** book, it was bright orange. He started to read it and giggle.

After few minutes of thinking, Naruto understood what Kakashi was doing. 'So to pass this test, I have to act like a team player.'

'What the hell is he reading? Is he not taking Uchiha seriously?' Sasuke though and when he was about to attack Kakashi, Naruto appeared behind him.

"Sasuke."

Sasuke turn around to see Naruto looking at him. He didn't even felt his pressence. He took a defence stance, "What do you want?"

"Nothing much, just to pass this test. Did you notice something is odd about this test?"

"Yeah, I remember father saying that teams are always four people."

"Yes exactly, I think Kakashi is try to pit us against each to see if we betray one another to complete mission."

"Yes, That does sound right"

"I know, you don't want to work together to pass the test but we have to Sasuke, It's not like I want to work with you either."

Both of them nodded to each other.

"We need to go and find Sakura is well." Naruto said.

"Why? She is useless." Sasuke asked.

"Oh god I know but we have to work as team to pass."

Sasuke understood, what he said, "So do you know where she is?"

"Yeah, 2 o'clock, 50 meters away from here." Naruto said. Both of them made there way to Sakura.

'Hmm, I guess Naruto figured it out, and Sasuke agreed to work with him. Naruto, Good job.' Kakashi though while smiling and glanced at where Sasuke and Naruto were.

Sakura was looking for Sasuke, suddenly Sasuke and Naruto appeared in front of her. Before any of the boys can say anything, Sakura went berserk, "Sasuke-kun, Why did you team up with that creep." Naruto's eye twitched, 'Sakura Haruno, before I leave this village, I will kill you myself!'

"Silence Sakura. The point of this test is to team up. There is no way genin can beat jounin so he wants to see if we betray one another to pass the test."

"I, agree with Naruto." Sasuke said but he didn't look happy about that Naruto, knew before him. Sakura just noded

"So lets make up a plan." Naruto said.

After 10 minutes of discussion, they came out with a plan.

Naruto appeared front of Kakashi. 'I have to act like genin, I need to become slower and use low level jutsus." Naruto thought and start to run to Kakashi.

Naruto jump into the air and tried to kick Kakashi on his head but Kakashi blocked it with his shoulder then he pushed Naruto away, Naruto done back-flip and landed on the ground. Sakura appeared few meters behind and start to run to Kakashi. Naruto done some hand signs, "**Earth Release: Feet Prison Jutsu"** Naruto yelled. Sudden earth sucked Kakashi's feet to the ground. Kakashi turn around to see Sakura was still coming at him with a kunai in her hand. Kakashi took out his kunai and throw it at her but kunai went through her. 'Clone Technique' Kakashi thought but he was too late. Sasuke was in the air and he shouted **"Fire Release: Great Fireball Jutsu."** Sasuke breath out a fireball, that was aim at Kakashi. Before fireball hit Kakashi, Kakashi broke the feet prison jutsu and dash away from the fire but when he was getting away he notice something went past him fast, it look like Naruto.

Kakashi stopped after he was far away from the fire. "Good planing but it failed." Kakashi said while pointing out the obvious.

All three of them were standing together and smiling, "What do you mean failed?" Naruto said while showing his right hand that held two bells.

Kakashi was shocked, so that what he seen was Naruto, he was really fast. "So what are you going to do? Who are you going to give the extra bell?" Kakashi said.

Naruto smiled. "Kakashi-sensei we already now this was a team work test, you just wanted to see we betray one another for to complete the test. Am right?"

"Hahaha. Yeah, you're right, well then you all passed." Kakashi announced.

Sakura was happy that she wasn't going back to academy and know she will be with Sasuke, forever, at least this what she thought. Sasuke just said 'hn' but he was kind a piss off that Naruto was the one came out with plan and he act like he was the superior one. Naruto didn't care much, he knew he will pass.

"Okay, we start training tomorrow and will do some D rank missions. For know, go home and chill." Kakashi said and turn into smoke.

"Say Sasuke-kun, Should we go on a date?" Sakura asked with desperate tone.

"No." Sasuke sounded serious.

While Naruto was already gone. He was heading to his lab to make the curse seal part of him so that he can put on people.

**.:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:.**

Naruto Arrived to his lab. 'Finally with this, I can offer people power who will join me' Naruto thought while he had a evil smile. Naruto sat down on a chair, while he hold is left arm out. With his right hand, he inject something to his left arm. Suddenly his veins turn into black and he started to scream like if his limbs getting pulled apart. Thanks to sound seal that was all over the place, no one heard his screams.

Tomorrow morning, when he woke up, he was on the floor but he could feel the curse seal made him stronger.

**.:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:. .:I I:.**

**End of the Chapter...**

Finally Another Chapter is finish. I will update new chapter soon as possible. I will waiting for your review so please don't forget leave a review

I am open to ideas for future chapters so if you want to share your ideas then leave a review or private msg me.

Naruto X ? = well I am not sure about the pairings so I will be waiting for your reviews on this matter.


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